Additional files

Additional file 1:

Supplementary Information and Supplementary Tables S1, S2 and S5. Supplementary Materials, Methods and References. Supplementary Table S1: number
of mapped junctions contributed uniquely by the combinatorial database (Comb DB only)
or TopHat (TopHat only) and the number of mapped junctions detected by both the combinatorial
database and TopHat (Both). Supplementary Table S2: the contribution of TopHat to
the number of junctions predicted to generate a PTC versus all junctions (minimum
of three reads per junction). Supplementary Table S5: deregulation of core splice
factors. Gene FC indicates the change in mRNA levels for all the isoforms for the
particular gene between KO and WT.

Supplementary Figure S2. Histogram showing distance from normal stop codon to the 3' end of RefSeq genes
with stops in final exon, and distances to nearest downstream exon-exon junction for
genes with stop codons in the second to last exon.